/rcsb/ligands

POST /api/rcsb/ligands

Price: 1 credit

Get a PDB chemical component — a ligand, cofactor, ion or modified residue — by its code

How to use it

The code is the short PDB chemical component identifier used inside structures, such as HEM or ATP, matched case-insensitively; it is not a ChEMBL, DrugBank or PubChem identifier, though `drugbank_id` and `related_resources` give the bridge to those. `type` distinguishes a free ligand from a modified amino acid or nucleotide, so components that only ever appear inside a polymer chain are in here too.

Parameters

• access-token string required

Request body

• timeout integer — Max scrapping execution timeout (in seconds) (default: 300; min: 20; max: 1500)
• ligand string required — PDB chemical component identifier, such as HEM or ATP (examples: "HEM", "ATP"; minLength: 1; maxLength: 5)

Response

• @type string (default: "RcsbLigand")
• id string (default: "")
• name string (default: "")
• formula string (default: "")
• formula_weight number nullable
• type string (default: "")
• formal_charge integer nullable
• is_ambiguous boolean nullable
• release_status string (default: "")
• processing_site string (default: "")
• replaces string (default: "")
• parent_component_ids array (default: [])
• one_letter_code string (default: "")
• initial_deposition_date string (default: "")
• initial_release_date string (default: "")
• revision_date string (default: "")
• smiles string (default: "")
• smiles_stereo string (default: "")
• inchi string (default: "")
• inchi_key string (default: "")
• drugbank_id string (default: "")
• atc_codes array (default: [])
• atom_count integer nullable
• heavy_atom_count integer nullable
• chiral_atom_count integer nullable
• bond_count integer nullable
• aromatic_bond_count integer nullable
• synonyms array (default: [])
  • @type string (default: "RcsbLigandSynonym")
  • name string (default: "")
  • type string (default: "")
  • provenance_source string (default: "")
• identifiers array (default: [])
  • @type string (default: "RcsbLigandIdentifier")
  • identifier string (default: "")
  • type string (default: "")
  • program string (default: "")
  • program_version string (default: "")
• descriptors array (default: [])
  • @type string (default: "RcsbLigandIdentifier")
  • identifier string (default: "")
  • type string (default: "")
  • program string (default: "")
  • program_version string (default: "")
• related_resources array (default: [])
  • @type string (default: "RcsbLigandRelatedResource")
  • resource_name string (default: "")
  • accession_code string (default: "")
  • mapping_method string (default: "")
• targets array (default: [])
  • @type string (default: "RcsbLigandTarget")
  • name string (default: "")
  • interaction_type string (default: "")
  • reference_database_name string (default: "")
  • reference_database_accession string (default: "")
  • target_actions array (default: [])
  • provenance_source string (default: "")
• annotations array (default: [])
  • @type string (default: "RcsbAnnotation")
  • id string (default: "")
  • name string (default: "")
  • type string (default: "")
  • description string (default: "")
  • provenance_source string (default: "")
  • assignment_version string (default: "")
  • lineage array (default: [])
    • @type string (default: "RcsbLineageNode")
    • id string (default: "")
    • name string (default: "")
    • depth integer nullable
  • additional_properties array (default: [])
    • @type string (default: "RcsbNamedValues")
    • name string (default: "")
    • values array (default: [])
• features array (default: [])
  • @type string (default: "RcsbLigandFeature")
  • type string (default: "")
  • value string (default: "")
  • source string (default: "")
• audit array (default: [])
  • @type string (default: "RcsbLigandAudit")
  • action_type string (default: "")
  • date string (default: "")

Errors

• 422 — The request body did not validate Check the fields against this schema. A URN with the wrong prefix is the most common cause.
• 408 — The request ran past its time limit Raise `timeout` in the request body, up to the maximum this endpoint documents. Lowering `count` or turning off the `with_*` flags also helps, because less work finishes sooner.
• 412 — Chemical component not found Retrying will not help: either the entity does not exist, or the input points at a different one.
• 429 — Too many requests: a rate limit or a usage window is exhausted When the response carries an X-Retry-After header, wait that many seconds and retry: the same number is in the body as `detail.retry_after`, and the limit clears once that window passes. The message in the body names the limit that was hit.
• 500 — Something broke on our side Retrying will not help. If it keeps happening, send us the X-Request-ID from the response headers.
• 529 — Rate limit reached, or the endpoint is overloaded Wait at least 30 seconds, then retry.

Response headers

• X-Error — Error message text (present only on error)
• X-Request-ID — Unique request identifier
• X-Execution-Time — Execution time in seconds
• X-Result-Count — How many records the body carries. 0 means an empty result, which is a normal answer and not by itself an error. A non-zero count can come back together with X-Error when the failure happened partway through — read this header and X-Error independently.
• X-Total-Available-Results — How many records exist for this query, when the endpoint can say. On a `dry_run` request this is the answer and the body is empty. It saturates: the endpoint's documented maximum means 'at least that many', any smaller number is exact.
• X-Warning — Present when the request body carried keys this endpoint does not document. They were ignored, so any filter you meant to apply through them did not apply. Check the spelling against this schema and retry.
• X-Retry-After — Seconds to wait before retrying. Present only on 429.